bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intestinal microbiota modulation and improved growth in pigs with post-weaning antibiotic and ZnO supplementation but only subtle microbiota effects with Bacillus altitudinis
Authors: Crespo-Piazuelo Daniel , Lawlor Peadar G. , Ranjitkar Samir , Cormican Paul , Villodre Carmen , Bouwhuis Meike A. , Marsh Alan , Crispie Fiona , Rattigan Ruth , Gardiner Gillian E. 
Published: December 2021

AbstractThe objective was to evaluate the effect of dietaryBacillus altitudinisspore supplementation during day (D)0–28 post-weaning (PW) and/or D29–56 PW compared with antibiotic and zinc oxide (AB + ZnO) supplementation on pig growth and gut microbiota. Eighty piglets were selected at weaning and randomly assigned to one of five dietary treatments: (1) negative control (Con/Con); (2) probiotic spores from D29–56 PW (Con/Pro); (3) probiotic spores from D0–28 PW (Pro/Con); (4) probiotic spores from D0–56 PW (Pro/Pro) and (5) AB + ZnO from D0–28 PW. Overall, compared with the AB + ZnO group, the Pro/Con group had lower body weight, average daily gain and feed intake and the Pro/Pro group tended to have lower daily gain and feed intake. However, none of these parameters differed between any of the probiotic-treated groups and the Con/Con group. Overall, AB + ZnO-supplemented pigs had higherBacteroidaceaeandPrevotellaceaeand lowerLactobacillaceaeandSpirochaetaceaeabundance compared to the Con/Con group, which may help to explain improvements in growth between D15–28 PW. The butyrate-producing generaAgathobacter,FaecalibacteriumandRoseburiawere more abundant in the Pro/Con group compared with the Con/Con group on D35 PW. Thus, whilst supplementation withB. altitudinisdid not enhance pig growth performance, it did have a subtle, albeit potentially beneficial, impact on the intestinal microbiota.
Temporal refinement of 3D CNN semantic segmentations on 4D time-series of undersampled tomograms using hidden Markov models
Authors: Bellos Dimitrios , Basham Mark , Pridmore Tony , French Andrew P. 
Published: December 2021

AbstractRecently, several convolutional neural networks have been proposed not only for 2D images, but also for 3D and 4D volume segmentation. Nevertheless, due to the large data size of the latter, acquiring a sufficient amount of training annotations is much more strenuous than in 2D images. For 4D time-series tomograms, this is usually handled by segmenting the constituent tomograms independently through time with 3D convolutional neural networks. Inter-volume information is therefore not utilized, potentially leading to temporal incoherence. In this paper, we attempt to resolve this by proposing two hidden Markov model variants that refine 4D segmentation labels made by 3D convolutional neural networks working on each time point. Our models utilize not only inter-volume information, but also the prediction confidence generated by the 3D segmentation convolutional neural networks themselves. To the best of our knowledge, this is the first attempt to refine 4D segmentations made by 3D convolutional neural networks using hidden Markov models. During experiments we test our models, qualitatively, quantitatively and behaviourally, using prespecified segmentations. We demonstrate in the domain of time series tomograms which are typically undersampled to allow more frequent capture; a particularly challenging problem. Finally, our dataset and code is publicly available.
Structural and functional thalamocortical connectivity study in female fibromyalgia
Authors: Kim Dajung J. , Lim Manyoel , Kim June Sic , Chung Chun Kee 
Published: December 2021

AbstractDysfunctional thalamocortical interactions have been suggested as putative mechanisms of ineffective pain modulation and also suggested as possible pathophysiology of fibromyalgia (FM). However, it remains unclear which specific thalamocortical networks are altered and whether it is related to abnormal pain perception in people with FM. Here, we conducted combined vertex-wise subcortical shape, cortical thickness, structural covariance, and resting-state functional connectivity analyses to address these questions. FM group exhibited a regional shape deflation of the left posterior thalamus encompassing the ventral posterior lateral and pulvinar nuclei. The structural covariance analysis showed that the extent of regional deflation of the left posterior thalamus was negatively covaried with the left inferior parietal cortical thickness in the FM group, whereas those two regions were positively covaried in the healthy controls. In functional connectivity analysis with the left posterior thalamus as a seed, FM group had less connectivity with the periaqueductal gray compared with healthy controls, but enhanced connectivity between the posterior thalamus and bilateral inferior parietal regions, associated with a lower electrical pain threshold at the hand dorsum (pain-free point). Overall, our findings showed the structural thalamic alteration interacts with the cortical regions in a functionally maladaptive direction, leading the FM brain more responsive to external stimuli and potentially contributing to pain amplification.
Clinical effects of cervical conization with positive margins in cervical cancer
Authors: Nagao Yukari , Yokoi Akira , Yoshida Kosuke , Sumi Masanori , Yoshihara Masato , Tamauchi Satoshi , Ikeda Yoshiki , Yoshikawa Nobuhisa , Nishino Kimihiro , Niimi Kaoru , Kajiyama Hiroaki 
Published: December 2021

AbstractRadical surgery after cervical conization is a common approach for the treatment of cervical cancer. In some cases, disease progression is observed after positive margins at conization, but the effect of conization on disease progression remains unclear. Thus, the aim of this study was to investigate the clinical outcomes of positive margins at conization in cervical cancer. A total of 101 patients who underwent cervical conization before radical hysterectomy and pelvic lymph node dissection were considered eligible by reviewing medical records. The association between the positive margins and patient outcomes, including subsequent lymph node metastasis, was evaluated. The rate of lymphovascular space invasion (LVSI) positivity at radical surgery was significantly higher in patients with positive margins (p = 0.017) than in those with negative margins, although there was no significant difference in the rate of pelvic lymph node metastasis (p = 0.155). Moreover, there was no significant difference in the overall survival or progression-free survival between the two groups (p = 0.332 and 0.200, respectively). A positive margin at conization presented no significant prognostic disadvantage; thus, diagnostic conization is one of the most suitable treatment options for early-stage cervical cancer that is difficult to accurately assess.
Routine COVID-19 testing may not be necessary for most cancer patients
Authors: Motlagh Ali , Elmi Fatemeh , Yamrali Maisa , Ranjbar Mansour , Azmin Mehrdad , Moshiri Farzaneh , Hamelmann Christoph , Slama Slim , Tavakoli Nadia , Hammerich Asmus , Pourghazian Nasim , Soleymani Nejad Marzeyeh , Mafi Ahmad , Azadeh Payam , Aghajanizadeh Maryam , Ostovar Afshin , Raeisi Alireza , Malekzadeh Reza 
Published: December 2021

AbstractCancer patients are at risk for severe complications or death from COVID-19 infection. Therefore, the need for routine COVID-19 testing in this population was evaluated. Between 1st August and 30th October 2020, 150 cancer patients were included. Symptoms of COVID-19 infection were evaluated. All eligible individuals went through RT-PCR and serological tests for COVID-19. At the same time, 920 non-cancer patients were recruited from a random sample of individuals who were subject to routine molecular and anti-body screening tests. Of 150 cancer patients, 7 (4.7%) were RT-PCR positive. Comorbidity made a significant difference in the RT-PCR positivity of cancer patients, 71.4% positive versus 25.8% negative (P-value = 0.02). The average age for negative and positive groups was 53.3 and 58.2 respectively (P-value = 0.01). No significant difference was observed between cancer and non-cancer patients regarding COVID-19 antibody tests. However, cancer patients were 3 times less likely to have a positive RT-PCR test result OR = 0.33 (CI: 0.15–0.73). The probability of cancer patients having a positive routine test was significantly lower than non-cancer patients, and the concept that all cancer patients should be routinely tested for COVID-19 may be incorrect. Nevertheless, there may be a subgroup of patients with comorbidities or older age who may benefit from routine COVID-19 testing. Importantly, these results could not be subjected to multivariate analysis.
Mathematical modeling and multivariate analysis applied earliest soybean harvest associated drying and storage conditions and influences on physicochemical grain quality
Authors: Lima Roney Eloy , Coradi Paulo Carteri , Nunes Marcela Trojahn , Bellochio Sabrina Dalla Corte , da Silva Timm Newiton , Nunes Camila Fontoura , de Oliveira Carneiro Letícia , Teodoro Paulo Eduardo , Campabadal Carlos 
Published: December 2021

AbstractAnticipating the harvest period of soybean crops can impact on the post-harvest processes. This study aimed to evaluate early soybean harvest associated drying and storage conditions on the physicochemical soybean quality using of mathematical modeling and multivariate analysis. The soybeans were harvested with a moisture content of 18 and 23% (d.b.) and subjected to drying in a continuous dryer at 80, 100, and 120 °C. The drying kinetics and volumetric shrinkage modeling were evaluated. Posteriorly, the soybean was stored at different packages and temperatures for 8 months to evaluate the physicochemical properties. After standardizing the variables, the data were submitted to cluster analysis. For this, we use Euclidean distance and Ward's hierarchical method. Then defining the groups, we constructed a graph containing the dispersion of the values of the variables and their respective Pearson correlations for each group. The mathematical models proved suitable to describe the drying kinetics. Besides, the effective diffusivity obtained was 4.9 × 10–10 m2 s−1 promoting a volumetric shrinkage of the grains and influencing the reduction of physicochemical quality. It was observed that soybean harvested at 23% moisture, dried at 80 °C, and stored at a temperature below 23 °C maintained its oil content (25.89%), crude protein (35.69%), and lipid acidity (5.54 mL). In addition, it is to note that these correlations' magnitude was substantially more remarkable for the treatments allocated to the G2 group. Furthermore, the electrical conductivity was negatively correlated with all the physicochemical variables evaluated. Besides this, the correlation between crude protein and oil yield was positive and of high magnitude, regardless of the group formed. In conclusion, the early harvest of soybeans reduced losses in the field and increased the grain flow on the storage units. The low-temperature drying and the use of packaging technology close to environmental temperatures conserved the grain quality.
Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract
Authors: Patel Sunita , Hosur Ramakrishna V. 
Published: December 2021

AbstractCrystallins are ubiquitous, however, prevalence is seen in eye lens. Eye lens crystallins are long-lived and structural intactness is required for maintaining lens transparency and protein solubility. Mutations in crystallins often lead to cataract. In this study, we performed mutations at specific sites of M-crystallin, a close homologue of eye lens crystallin and studied by using replica exchange molecular dynamics simulation with generalized Born implicit solvent model. Mutations were made on the Ca2+ binding residues (K34D and S77D) and in the hydrophobic core (W45R) which is known to cause congenital cataract in homologous γD-crystallin. The chosen mutations caused large motion of the N-terminal Greek key, concomitantly broke the interlocking Greek keys interactions and perturbed the compact core resulting in several folded and partially unfolded states. Partially unfolded states exposed large hydrophobic patches that could act as precursors for self-aggregation. Accumulation of such aggregates is the potential cause of cataract in homologous eye lens crystallins.
Geographic footprints of life expectancy inequalities in the state of Geneva, Switzerland
Authors: Ladoy Anaïs , Vallarta-Robledo Juan R. , De Ridder David , Sandoval José Luis , Stringhini Silvia , Da Costa Henrique , Guessous Idris , Joost Stéphane 
Published: December 2021

AbstractThough Switzerland has one of the highest life expectancies in the world, this global indicator may mask significant disparities at a local level. The present study used a spatial cluster detection approach based on individual death records to investigate the geographical footprint of life expectancy inequalities in the state of Geneva, Switzerland. Individual-level mortality data (n = 22,751) were obtained from Geneva’s official death notices (2009–2016). We measured life expectancy inequalities using the years of potential life lost or gained (YPLLG) metric, defined as the difference between an individual’s age at death and their life expectancy at birth. We assessed the spatial dependence of YPLLG across the state of Geneva using spatial autocorrelation statistics (Local Moran’s I). To ensure the robustness of the patterns discovered, we ran the analyses for ten random subsets of 10,000 individuals taken from the 22,751 deceased. We also repeated the spatial analysis for YPLLG before and after controlling for individual-level and neighborhood-level covariates. The results showed that YPLLG was not randomly distributed across the state of Geneva. The ten random subsets revealed no significant difference with the geographic footprint of YPLLG and the population characteristics within Local Moran cluster types, suggesting robustness for the observed spatial structure. The proportion of women, the proportion of Swiss, the neighborhood median income, and the neighborhood median age were all significantly lower for populations in low YPLLG clusters when compared to populations in high YPLLG clusters. After controlling for individual-level and neighborhood-level covariates, we observed a reduction of 43% and 39% in the size of low and high YPLLG clusters, respectively. To our knowledge, this is the first study in Switzerland using spatial cluster detection methods to investigate inequalities in life expectancy at a local scale and based on individual data. We identified clear geographic footprints of YPLLG, which may support further investigations and guide future public health interventions at the local level.
Infant-gut associated Bifidobacterium dentium strains utilize the galactose moiety and release lacto-N-triose from the human milk oligosaccharides lacto-N-tetraose and lacto-N-neotetraose
Authors: Moya-Gonzálvez Eva M. , Rubio-del-Campo Antonio , Rodríguez-Díaz Jesús , Yebra María J. 
Published: December 2021

AbstractMuch evidence suggests a role for human milk oligosaccharides (HMOs) in establishing the infant microbiota in the large intestine, but the response of particular bacteria to individual HMOs is not well known. Here twelve bacterial strains belonging to the genera Bifidobacterium, Enterococcus, Limosilactobacillus, Lactobacillus, Lacticaseibacillus, Staphylococcus and Streptococcus were isolated from infant faeces and their growth was analyzed in the presence of the major HMOs, 2′-fucosyllactose (2′FL), 3-fucosyllactose (3FL), 2′,3-difucosyllactose (DFL), lacto-N-tetraose (LNT) and lacto-N-neo-tetraose (LNnT), present in human milk. Only the isolated Bifidobacterium strains demonstrated the capability to utilize these HMOs as carbon sources. Bifidobacterium infantis Y538 efficiently consumed all tested HMOs. Contrarily, Bifidobacterium dentium strains Y510 and Y521 just metabolized LNT and LNnT. Both tetra-saccharides are hydrolyzed into galactose and lacto-N-triose (LNTII) by B. dentium. Interestingly, this species consumed only the galactose moiety during growth on LNT or LNnT, and excreted the LNTII moiety. Two β-galactosidases were characterized from B. dentium Y510, Bdg42A showed the highest activity towards LNT, hydrolyzing it into galactose and LNTII, and Bdg2A towards lactose, degrading efficiently also 6′-galactopyranosyl-N-acetylglucosamine, N-acetyl-lactosamine and LNnT. The work presented here supports the hypothesis that HMOs are mainly metabolized by Bifidobacterium species in the infant gut.
Analysis at the single-cell level indicates an important role of heterogeneous global DNA methylation status on the progression of lung adenocarcinoma
Authors: Chen Quan-Fang , Gao Han , Pan Qing-Yun , Wang Ying-Ju , Zhong Xiao-Ning 
Published: December 2021

AbstractAberrant DNA modifications affect the tumorigenesis and progression of lung cancer. However, the global methylation status of tumor cells and the heterogeneous methylation status of cells within the same tumor need further study. We used publicly available single-cell RNAseq data to investigate the impact and diversity of global methylation status on lung adenocarcinoma. Clustering cells into subgroups and cell differentiation pseudotime analysis, based on expression profile, demonstrated that the global methylation status was crucial to lung adenocarcinoma function and progression. Hypermethylated tumor cells had increased activity related to the hypoxia response. Hyper- and hypomethylated cells indicated upregulation in pathways involving focal adhesion and cell junctions. Pseudotime analysis showed that cell clusters with unique methylation activities were located at the ends of the putative trajectories, suggesting that DNA methylation and demethylation activities were essential to tumor cell progression. Expression of SPP1 was associated with the global methylation status of tumor cells and with patient prognosis. Our study identified the importance and diversity of global DNA methylation status by analysis at the single-cell level. Our findings provide new information about the global DNA methylation status of tumor cells and suggest new approaches for precision medical treatments for lung adenocarcinoma.
In vivo antimicrobial activity of 0.6% povidone-iodine eye drops in patients undergoing intravitreal injections: a prospective study
Authors: Tognetto Daniele , Pastore Marco R. , Belfanti Lorenzo , Merli Riccardo , Vinciguerra Alex L. , Busetti Marina , Barbati Giulia , Cirigliano Gabriella 
Published: December 2021

AbstractTo investigate the antimicrobial activity of a preservative-free 0.6% povidone-iodine eye drop as an antiseptic procedure in decreasing the conjunctival bacterial load in eyes scheduled for intravitreal treatment and to compare its efficacy to the untreated fellow eye used as the control group. Prospective cohort analysis in which 208 patients received preservative-free 0.6% povidone-iodine eye drops three times a day for three days before intravitreal injection. Before and after the prophylactic treatment, a conjunctival swab was collected from both the study eye and the untreated contralateral eye, used as control. The swab was inoculated on different culture media and the colony-forming units were counted. Bacteria and fungi were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Treatment with 0.6% povidone-iodine eye drops significantly reduced the conjunctival bacterial load from baseline (p < 0.001 for blood agar and p < 0.001 for chocolate agar) with an eradication rate of 80%. The most commonly isolated pathogen at each time-point and in both groups was coagulase-negative Staphylococci, isolated in 84% of the positive cultures. The study provides evidence about the effectiveness of 0.6% povidone-iodine eye drops treatment in reducing the conjunctival bacterial load in eyes scheduled for intravitreal treatment.
A multicenter, randomized, active-controlled, clinical trial study to evaluate the efficacy and safety of navigation guided balloon Eustachian tuboplasty
Authors: Choi Sung-Won , Oh Se-Joon , Kim Yehree , Kwak Min Young , Suh Myung-Whan , Park Moo Kyun , Lee Chi Kyou , Park Hong Ju , Kong Soo-Keun 
Published: December 2021

AbstractTo assess the safety and efficacy of navigation-guided balloon Eustachian tuboplasty (BET) compared to medical management (MM) alone in patients with chronic Eustachian tube dilatory dysfunction (ETD). This is a prospective, multicenter, 1:1 parallel-group, randomized controlled trial (RCT). It aims to assess the efficacy of navigation-guided BET compared to MM alone in patients with chronic ETD. The primary outcome measure was an improvement in the Eustachian tube dysfunction questionnaire (ETDQ)-7 score at the 6-week follow-up compared with baseline. Secondary outcome measures included changes in the signs and symptoms during the follow-up, changes in the score for each subcategory of ETDQ-7, type of tympanometry, pure tone audiometry, and the availability of a positive modified Valsalva maneuver. Navigation-guided BET was safely performed in all patients. A total of 38 ears of 31 patients (19 ears of 16 patients in the BET group and 19 ears of 15 patients in the control group) completed the planned treatment and 6 weeks of follow-up. More patients in the BET group (1.99 ± 0.85) had less symptomatic dysfunction than in the control group (3.40 ± 1.29) at 6 weeks post-procedure (P = 0.001). More patients experienced tympanogram improvement in the BET group at 6 weeks compared to the control group (36.5% vs. 15.8%) with a positive modified Valsalva maneuver (36.6% vs. 15.8%, P = 0.014). Additionally, air–bone gap change was significantly decreased in the BET group compared to the control group at the 6-week follow-up visit (P = 0.037). This prospective, multicenter, RCT study suggests that navigation-guided BET is a safe and superior treatment option compared to MM alone in patients with chronic ETD.
Harnessing the ambiphilicity of silyl nitronates in a catalytic asymmetric approach to aliphatic β3-amino acids
Authors: Das Sayantani , Mitschke Benjamin , De Chandra Kanta , Harden Ingolf , Bistoni Giovanni , List Benjamin 
Published: December 2021

AbstractNitronate anions, formally generated by α-deprotonating the corresponding nitroalkanes, are highly nucleophilic and versatile intermediates in many carbon–carbon bond-forming reactions. In contrast, the corresponding silyl nitronates are ambiphilic and react, at the same carbon atom, with both electrophiles and nucleophiles. However, while their nucleophilicity has been well exploited in catalytic enantioselective reactions with imines and aldehydes, utilizing the electrophilicity of silyl nitronates in asymmetric synthesis has remained elusive. Here we report the facile, efficient and general reactivity of readily available silyl nitronates with silyl ketene acetals, catalysed by highly Lewis-acidic and confined silylium imidodiphosphorimidate catalysts. The products of this reaction, so-called nitroso acetals, are obtained in excellent enantioselectivity and can be easily converted into N-Boc-β3-amino acid esters in a single step.