bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-course Alterations of Gut Microbiota and Short-chain Fatty Acids After Short-term Lincomycin Exposure in Young Swine
Authors: Tang Shanlong , Zhang Shunfen , Zhong Ruqing , Su Dan , Xia Bing , Liu Lei , Chen Liang , Zhang Hongfu 
Published: August 2021

Abstract
Background: Increasing evidence suggests that antibiotic administration causes gut injury, nutrient digestion, immune regulation, and colonization resistance against pathogens due to the disruption of gut microbiota. However, the time-course effects of therapeutic antibiotics on alterations of gut microbes and short-chain fatty acid in young swine are still unknown. In this study, twenty piglets were assigned into two groups and fed commercial diets with or without lincomycin in the first week for a 28-day trial period. Results: Data showed that one-week lincomycin exposure did reduce the body weight on day 14 (p = 0.0450) and 28 (p = 0.0362). The alpha-diversity notably reduced after one-week lincomycin treatment, then gradually raised and reached the control group level in the second week on cessation of lincomycin exposure, indicated by the variation of Sobs, Chao, Shannon, and ACE index (p < 0.05). Beta-diversity analysis revealed that the distinct microbial cluster existed persistently for the whole trial period between two groups (p < 0.001). The relative abundance of most microbes including fiber-degrading (e.g., Agathobacter, Coprococcus, etc.), beneficial (e.g., Lactobacillus, Mitsuokella, etc.), or pathogenic bacteria (e.g., Terrisporobacter, Lachnoclostridium, etc.) decreased and the concentration of short-chain fatty acids also diminished in the feces of one-week lincomycin-administrated young swine (LDA score > 3). After the lincomycin administration stopped, the state of gut dysbiosis gradually recovered and formed new gut-microbe homeostasis distinct from microbial homeostasis of young pigs unexposed to lincomycin. The increased presence of potential pathogens, such as Terrisporobacter, Negativibacillus, Escherichia-Shigella, etc. and decreased beneficial bacteria such as Lactobacillus, Agathobacter were observed in new homeostasis reshaped by short-lincomycin administration (LDA score > 3 or p < 0.05), adversely affecting gut development and health of young pigs. Conclusion: Collectively, these results suggested that severe disruption of the commensal microbiota occurred after short-term lincomycin exposure or termination of lincomycin exposure in young swine. Our study depicts the change rule of gut microbiota in young animals under the condition of short-term lincomycin treatment, providing basic data for evaluating the harmful impact on gut microbe of young animals.
Parallel Approach of Schr¨Odinger Based Quantum Corrections for Ultrascaled Semiconductor Devices
Authors: Espiñeira G. , Garc´ıa-Loureiro A. J. , Seoane N. 
Published: August 2021

Abstract
In the current technology node, purely classical numerical simulators lack the precision needed to obtain valid results. At the same time, the simulation of fully quantum models can be a cumbersome task in certain studies such as device variability analysis, since a single simulation can take up to weeks to compute and hundreds of device configurations need to be analyzed to obtain statistically significative results. A good compromise between fast and accurate results is to add corrections to the classical simulation that are able to reproduce the quantum nature of matter. In this context, we present a new approach of Schrödinger equation-based quantum corrections. We have implemented it using Message Passing Interface (MPI) in our in-house built semiconductor simulation framework called VENDES, capable of running in distributed systems that allow for more accurate results in a reasonable time frame. Using a 12 nm gate length Gate-AllAround Nanowire FET (GAA NW FET) as an application example, the new implementation shows an almost perfect agreement in the output data with less than a 2% difference between the cases using 1 and 16 processes. Also, a reduction of up to 98% in the computational time has been found comparing the sequential and the 16 process simulation. For a reasonably dense mesh of 150k nodes, a variability study of 300 individual simulations, can be now performed with VENDES in approximately 2.5 days instead of an estimated sequential execution of 137 days.
Open Nucleus Breeding Strategy for Fogera Cattle Breed in Ethiopia: Achievements and Lessons Learnt
Authors: Sendeku Assemu Tesfa , Tilahun Mekonnen , Asmare Zelalem , Kassahun Demelash , Bimerew Tewodross , Mengesha Wondimagegn , Bitew Addisu , Lakew Eyasu , Meseret Mulugeta 
Published: August 2021

Abstract
Fogera cattle are one of the promising indigenous milk type local breed of Ethiopia. The objective of this paper was to evaluate the performance of Fogera breed under open nucleus breeding scheme. The work was done in two purposively selected districts (Gondar Zuria and Fogera) with community-based breed productivity improvement (CBBPI) as an approach. The collected data was analysed by GLM procedure of SAS for fixed factors estimation. Genetic parameters estimate was made by ASREML software for heritability and correlation. The overall milk yield of the nucleus herd was 2.26 ± 0.794 litter. From the total herd, best 10% and 25% of them give a respective milk yield of 3.31 and 2.87 litter; and some elite cows give an average of 5.45 ± 0.73 litter with a maximum yield of eight litters per day. The overall birth and weaning weight of nucleus herd calves was 21.30 ± 0.06 and 103.66 ± 0.59kg, respectively. Heritability for birth and weaning weight was 0.24 ± 0.09 and 0.18 ± 0.05, respectively. The phenotypic and genotypic correlation with their respective standard error between birth and weaning weight was 0.0613 ± 0.0075 and 0.0712 ± 0.0343, respectively. For CBBPI program, 17 pure Fogera bulls were distributed to the two districts. The birth and weaning weight of the village calves was 23.77 ± 0.21 and 85.89 ± 1.07, respectively. Through the program, above 1000 households were benefiting through the breeding program, health, forage development and grazing land management. To share the achievements of the results in CBBPI program, popularization through filed days and innovation platforms; and documentation of each step via publications, videos and pictures was done. From the result, it can be concluded that the strategy implemented for the breed conservation “open nucleus breeding scheme” had shown progressive results and improvement was recorded. To widen the result and improve the livelihood of the farmer, scaling up of the activity should better be planned with stakeholders.
Early Experience of Atezolizumab Plus Bevacizumab Therapy in Japanese Patients With Unresectable Hepatocellular Carcinoma in Real-world Practice
Authors: Hayakawa Yuka , Tsuchiya Kaoru , Kurosaki Masayuki , Yasui Yutaka , Kaneko Shun , Tanaka Yuki , Ishido Shun , Inada Kento , Kirino Sakura , Yamashita Koji , Nobusawa Tsubasa , Matsumoto Hiroaki , Kakegawa Tatsuya , Higuchi Mayu , Takaura Kenta , Tanaka Shohei , Maeyashiki Chiaki , Tamaki Nobuharu , Nakanishi Hiroyuki , Itakura Jun , Takahashi Yuka , Asahina Yasuhiro , Okamoto Ryuichi , Izumi Namiki 
Published: August 2021

Abstract
Background: We aimed to investigate the efficacy and safety of atezolizumab plus bevacizumab therapy in patients with unresectable hepatocellular carcinoma (u-HCC) based on whether they had previously received systemic therapy, as well as the association of atezolizumab plus bevacizumab with early alpha-fetoprotein (AFP) response in real-world practice. Methods: A total of 52 patients with u-HCC were treated with atezolizumab plus bevacizumab between October 2020 and April 2021. The Response Evaluation Criteria in Solid Tumors (RECIST) and modified RECIST were used to evaluate radiological responses. Results: The patients received atezolizumab plus bevacizumab as 1st-line (n = 23), 2nd-line (n = 16), 3rd-line (n = 6), 4th-line (n = 3), 5th-line (n = 3), or 6th-line (n = 1) therapy. The objective response rate and disease control rate in all patients were 18.4% and 63.2%, respectively. Sixteen patients experienced no adverse events (AEs), whereas 4 patients discontinued therapy due to AEs. The median time to progression (TTP) was significantly longer among patients receiving atezolizumab plus bevacizumab as 1st-line therapy than in patients receiving atezolizumab plus bevacizumab as later-line therapy (P = 0.02). Patients with an AFP response (reduction ≥20% from baseline) at 6 weeks had a significantly longer TTP than those without an AFP response (P = 0.02). Conclusion: Patients who received atezolizumab plus bevacizumab as 1st-line therapy had better clinical outcome than those who received atezolizumab plus bevacizumab in later lines. The AFP response at 6 weeks could be a predictor of disease progression.
Database Development and Statistical Analysis of Survival in a Clinical and Historical Coort of Dogs Affected by Myxomatous Mitral Valve Disease Treated With Different Therapeutic Protocols Using Causal Inference Techniques
Authors: Bagardi Mara , Palermo Valentina , Locatelli Chiara , Colombo Fabio Maria , Pazzagli Laura , Brambilla Paola Giuseppina 
Published: August 2021

Abstract
The aim of this work was to retrospectively evaluate the influence of different therapeutic protocols (loop diuretics, ACE-inhibitors, spironolactone +/- pimobendan) on the survival time (ST) of dogs with myxomatous mitral valve disease at different stages using an Inverse Probability Weighting (IPW) analysis. An IPW method was used to minimize confounding and IPW weighted time-repeated logistic model was used to approximate survival curves (SCs) and calculate survival differences. Subjects were allocated into cases (CA) and controls (CO). Dogs in American College of Veterinary Internal Medicine (ACVIM) B2 class treated with pimobendan (+/- ACE-inhibitors) were selected for the CA group, as well as symptomatic patients (ACVIM class C) threated with triple (furosemide, ACE-inhibitor, pimobendan) or quadruple (furosemide, ACE-inhibitor, pimobendan and spironolactone) therapy. The CO group included ACVIM class B2 dogs not treated with any medication and ACVIM C dogs treated with a combination of furosemide and ACE-inhibitor/spironolactone without pimobendan.The SC of the CA group crossed the CO group at 1634 days. The difference between the two SCs at the time of maximum survival difference in favour of the CO group was 11.3% (CI 1.7%–20.9%) (significant), in favour of the CA group was 3.9% (CI -8.6%–16.4%) (not significant) and at the mean ST was 3.6% (CI -8.5%–15.7%) (not significant) in favour of the CA group. For times greater than 1634 days the survival was in favour of the CA group, there were no statistically significant differences in survival in favour of the CA group in this clinical population.
Degradation Dynamics of Quantum Dots in White LED Applications
Authors: Chen Hsiao-Chien , Tan Cher Ming , Shabir Abdul , Singh Preetpal , Wang Kai 
Published: August 2021

Abstract
Quantum dots (QDs) are being investigated in a hybrid white light LED structure which inculcates phosphor in the package with blue LED chip as light source. Upon prolong operation, degradation of CdS QDs is observed which can limit its practical applications. The degradation includes intensity reduction as well as emitted wavelength shift of the white light. Three stages of degradation are observed, namely an enhancement state where light intensity is observed to increase, followed by a rapid degradation stage where light intensity decreases rapidly, and finally a slower degradation state where light intensity degradation rate slows down and continue till end of test.In this work, the degradation of CdS QDs is analyzed using various material analysis tools. Density functional theory (DFT) calculation is performed to confirm the spectroscopy results. It is found that the time evolving degradation of QDs begins from the oxidation of sulfur vacancy of CdS QDs by nearby oxygen atoms due to the imperfection of the protective coating around the QDs in combination of the presence of blue light, and this oxidation renders a transformation of CdS into CdO at the initial state. The final stage is the formation of CdSO4 via some intermediate processes.
Do Vaccinated People Reduce Their Precautionary Behaviours? A Test on a British Cohort
Authors: Desrichard Olivier , Moussaoui Lisa , Ofosu Nana 
Published: August 2021

Abstract
Background.There is a risk that people vaccinated against COVID-19 will drop out or reduce their behaviours (i.e. a phenomenon of risk homeostasis). Our aim is to assess the occurrence of this effect in a cohort of UK participants who were interviewed 141 days before and 161 days after the start of the vaccination programme.Methods.Of the 7651 people who could be followed up before and after the start of the programme and whose vaccination status was known, 178 had not received any injection and 583 were more or less advanced in the process (one vs. two doses since less vs. more than 14 days). The frequency of 14 precautionary behaviours was assessed at both times of measurement, as well as potential covariates (gender, age, comorbidities and history of COVID-19).Findings.Controlling for covariates, we found no decrease in precautionary behaviours, including among vaccinated individuals, regardless of how far along they were in the process.Interpretation.The results observed in this sample show that a massive change in behaviour among vaccinated individuals does not threaten the fight against the COVID-19 pandemic. The pressure to adopt precautionary behaviours remains strong and probably prevents the emergence of a risk homeostasis effect. Nevertheless, communication on the importance of precautionary behaviour should be maintained so that it does not regress in the long term.
Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny
Authors: Technau Ulrich , Robb Sophia , Genikhovich Grigory , Montenegro Juan , Fropf Witney , Weinguny Lukas , He Shuonan , Chen Shiyuan , Lovegrove-Walsh Jessica , Hill Eric , Ragkousi Katerina , Praher Daniela , Fredman David , Moran Yehu , Gibson Matthew , Zimmermann Bob 
Published: August 2021

Abstract
Draft genome sequences of non-bilaterian species have provided important insights into the evolution of the metazoan gene repertoire. However, there is little information about the evolution of gene clusters, genome architectures and karyotypes during animal evolution. Here we report chromosome-level genome assemblies of two related anthozoan cnidarians, the sea anemones, Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence of the chromosomes between the two species. We show that, in contrast to Bilateria, Hox and NK clusters of investigated cnidarians are disintegrated, indicating that microsynteny conservation is largely lost. In line with that, we find no evidence for topologically associated domains, suggesting fundamental difference in long-range gene regulation compared to vertebrates. However, both sea anemone genomes show remarkable chromosomal conservation with other cnidarians, several bilaterians and the sponge Ephydatia muelleri, allowing us to reconstruct the putative cnidarian and metazoan chromosomes, consisting of 19 and 16 ancestral linkage groups, respectively. These data suggest that large parts of the ancestral metazoan genome have been retained in chromosomes of some extant lineages, yet, higher order gene regulation may have evolved only after the cnidarian-bilaterian split.
Transanal Endoscopic Microsurgical Submucosal Dissection: an Efficient Treatment Option for Giant Superficial Neoplastic Lesions of The Rectum
Authors: Kouladouros Konstantinos , Baral Jörg 
Published: August 2021

Abstract
PurposeThe resection of giant superficial neoplastic lesions of the rectum (>5 cm) is challenging and the ideal resection technique remains a controversial issue. Aim of our study is to assess the feasibility and outcomes of transanal endoscopic microsurgical submucosal dissection (TEM-ESD), a new hybrid technique, for the resection of giant superficial rectal neoplasms.MethodsWe retrospectively analyzed all cases of TEM-ESD for superficial rectal tumors >5cm performed in the Department of Surgery of the Municipal Hospital of Karlsruhe between 2010 and 2020. ResultsWe identified 43 cases matching our criteria (35 adenomas, 8 adenocarcinomas). The median size of the lesions was 75 mm, the median operating time was 81.5 min. En bloc resection was possible in all cases. In a follow-up period of 15 months there were 2 cases of local recurrence. ConclusionsTEM-ESD is a feasible and safe therapeutic option for the treatment of giant superficial rectal neoplasms.
Controversy on the Management of Patients Carrying RET p.V804M Mutation
Authors: Alzahrani Ali , Alswailem Meshael , Alghamdi Balgees , Rafiullah Rafiullah , Aldawish Mohammed , Al-Hindi Hindi 
Published: August 2021

Abstract
Context: RET p.V804M is classified as a moderate-risk mutation for familial medullary thyroid cancer (FMTC). There is a significant controversy on the management of patients carrying this mutation. We describe a family incidentally discovered to have this mutation during evaluation of a newborn with dysmorphic features. We provide a comprehensive literature review of RET p.V804M mutation. Results: The proband was born to a first-degree relative parents with hypertrophy of some parts of the body and vascular skin changes. Whole exome sequencing of DNA extracted from a skin biopsy showed a mutation in the PIK3CA (c.3132T>G, p.ASN1044LYS). This variant was not found in DNA extracted from blood. This confirmed the diagnosis CLOVES syndrome (Congenital Lipomatous Overgrowth, Vascular malformations, Epidermal nevi and Scoliosis, skeletal or spinal anomalies). Another incidentally found mutation in the skin biopsy and blood sample was RET p.V804M. Although there was no family history of MTC or MEN 2 syndromes, family screening revealed RET p.V804M mutation and FMTC in the proband's father, paternal grandmother, one sister and one aunt. There was significant interfamilial heterogeneity in age of presentation and pathology. Review of data showed that RET p.V804M mutation is an indolent mutation that may be discovered incidentally and associated with low risk of FMTC, usually at middle to old age. Conclusion: This and other recent studies raise questions about whether the American Thyroid Association (ATA) guidelines for management of patients with moderate risk RET mutations should also be applied to this seemingly “low” risk RET p.V804M mutation.
An Adapted One-dimensional Computational Approach for Irregular ROI Analysis Improves Osteosarcoma Classification
Authors: Djuričić Goran J. , Ahammer Helmut , Sopta Jelena P. , Kovač Jelena Djokić , Milošević Zorica , Apostolović Milan , Radulovic Marko 
Published: August 2021

Abstract
The authors have requested that this preprint be removed from Research Square.
Cis-acting Super-Enhancer lncRNAs as Biomarkers of Early-Stage Breast Cancer
Authors: Ropri Ali Salman , DeVaux Rebecca , Eng Jonah , Chittur Sridar V. , Herschkowitz Jason 
Published: August 2021

Abstract
Background Increased breast cancer screening over the past four decades has led to a substantial rise in the diagnosis of ductal carcinoma in situ (DCIS). Although DCIS lesions precede invasive ductal carcinoma (IDC), they do not always transform into cancer. The current standard-of-care for DCIS is an aggressive course of therapy to prevent invasive and metastatic disease resulting in over-diagnosis and over-treatment. Thus, there is a critical need to identify functional determinants of progression of DCIS to IDC to allow discrimination between indolent and aggressive disease. Recent studies show that super-enhancers, in addition to promoting other gene transcription, are themselves transcribed producing super-enhancer associated long noncoding RNAs (SE-lncRNAs). These SE-lncRNAs can interact with their associated enhancer regions in cis and influence activities and expression of neighboring genes. Furthermore, they represent a novel, untapped group of therapeutic targets.MethodsWith an integrative analysis of enhancer loci with global expression of SE-lncRNAs in the MCF10A progression series, we have identified differentially expressed SE-lncRNAs which can identify mechanisms for DCIS to IDC progression. Furthermore, cross-referencing these SE-lncRNAs with patient samples in the TCGA database, we have unveiled 31 clinically relevant SE-lncRNAs that potentially interact with their enhancer to regulate nearby gene expression. To complement SE-lncRNA expression studies, we conducted an unbiased global analysis of super-enhancers that are acquired or lost in progression. ResultsHere we designate SE-lncRNAs RP11-379F4.4 and RP11-465B22.8 as potential markers of progression of DCIS to IDC through regulation of the expression of their neighboring genes (RARRES1 and miR200b respectively). Moreover, we classified 403 super-enhancer regions in MCF10A normal cells, 627 in AT1, 1053 in DCIS, and 320 in CA1 cells. Comparison analysis of acquired/lost super-enhancer regions with super-enhancer regions classified in 47 ER positive patients, 10 Triple Negative Breast Cancer (TNBC) patients, and 11 TNBC cell lines reveal critically acquired pathways including STAT signaling and NF-kB signaling. In contrast, protein folding and local estrogen production are identified as major pathways lost in progression.ConclusionCollectively, these analyses identify differentially expressed SE-lncRNAs and acquired/lost super-enhancers in progression of breast cancer important for promoting DCIS lesions to IDC.
Molecular Epidemiological Characteristics of Human Rhinovirus Circulating in Shanghai, 2012 - 2020
Authors: Jiang Haixia , Yang Chunyi , Lu Yanping , Yi Zhigang , Wang Wei 
Published: August 2021

Abstract
Background

Human Rhinoviruses (HRVs) are a common respiratory virus causing acute exacerbations of asthma, chronic obstructive pulmonary disease (COPD) and other related diseases. The sequence of 5’ untranslated region (UTR) and VP4/VP2 coding region of the genome are usually analyzed to classify HRV as HRV-A, HRV-B and HRV-C. Given the interest for new viral strains, we identified the phylogenetic characteristics and molecular epidemiological analysis of human rhinovirus in Shanghai from 2012 to 2020.
Methods

6711 throat swabs and sputum samples from patients with acute respiratory infection (ARI) were collected, then the real-time reverse-transcriptase polymerase chain reaction (RT-PCR) method was used to detect HRV. And the fragment of 5 ' untranslated region (5'UTR) and the VP4/VP2 region were amplified for sequencing and gene typing.
Results

In total, 480/6711(7.2%) HRV-positive samples were detected from 2012–2020, in which 160 samples were further genotyped to HRV-A (109/160, 68.13%), HRV-B (32/160, 20.00%), HRV-C (19/160, 11.88%). We found 13 samples with unclassified results using 5'UTR. Then, these unclassified sample were genotyped to HRV-A and HRV-C by sequencing the VP4/VP2 region. The high incidence of HRV infection occurs in the fall and it is more prevalent in children than in adults.
Conclusion

Our study suggests that it is very significant to continuously detect and analyze the genotype distribution and epidemic trend of HRV, which can provide data support for disease prevention and treatment. And the 5' UTR and VP4/VP2 should be combined for HRV genotyping accurately.