bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical Choice for Different Types of Gallbladder Adenomyomatosis: An Initial Experience of 20 Years Laparoscopic Cholecystectomy
Authors: Pang Liwei , Wu Shuodong , Kong Jing 
Published: February 2020

Objectives:
The objective of this study was to compare the difference of clinical biochemical statistics in different types of gallbladder adenomyomatosis (GA). To investigate the different effects of patients between the 3 different types of GA.

Materials and Methods:
Retrospective analysis of the clinical data of the adenomyomatosis patients that come from our hospital between 2010 to 2018. According to the preoperative image (all cases are performed as elective surgery), it could be divided into 3 groups: group A: fundal (localized) type; group B: segmental type; group C: diffuse type. The number of each group is 136, 27, 17. We analyze the biochemical statistics (total bilirubin, direct bilirubin, serum bile acid, alanine aminotransferase, aspartate aminotransferase, cholinesterase, etc.) of the 3 groups to explore the difference in operative mode, operative time and prognosis between these 3 groups.

Results:
(1) In the liver function statistics, aspartate aminotransferase has the statistical significance (F=4.974, P=0.012); (2) And the diffuse adenomyomatosis might have a higher bile acid (F=6.048, P=0.005); (3) The segmental and diffuse adenomyomatosis is easier to be combined with stones (F=19.226, P<0.001); (4) The fundal adenomyomatosis seems to have a better prognosis: fewer hospital stay (F=4.519, P=0.018), fewer drainage time (F=6.575, P=0.004) and fewer complications (χ2=29.429, P<0.001).

Conclusions:
GA is a disease characterized by epithelial proliferation and hypertrophy of the muscles of the gallbladder wall with an outpouching of the mucosa into or through the thickened muscular layer and cannot be regarded as a precancerous lesion based on available evidence. As for asymptomatic GA, conservative treatment is recommended with ultrasound examinations twice a year. The fundal type GA can be treated by partial laparoscopic cholecystectomy. The segmental and diffuse-type should undergo a total laparoscopic cholecystectomy.
Private-public mappings in human prefrontal cortex
Authors: Bang Dan , Ershadmanesh Sara , Nili Hamed , Fleming Stephen M. 
Published: February 2020

ABSTRACTA core feature of human cognition is an ability to separate private states of mind – what we think or believe – from public actions – what we say or do. This ability is central to navigating social interactions in which different contexts often require different mappings between private states and public actions in order to minimise conflict and facilitate communication. Here we investigated how the human brain supports private-public mappings, using an interactive task which required subjects to adapt how they communicated their confidence about a perceptual decision to the social context. Univariate and multivariate analysis of fMRI data revealed that a private-public distinction is reflected in a medial-lateral division of prefrontal cortex – with lateral frontal pole (FPl) supporting the context-dependent mapping from a private sense of confidence to a public report. The concept of private-public mappings provides a promising framework for understanding flexible social behaviour.
Early reduction in PD-L1 expression predicts faster treatment response in human cutaneous leishmaniasis
Authors: Dey Nidhi S. , Senarathna Sujai , Somaratne Vijani , Madarasinghe Nayani , Seneviratne Bimalka , Forrester Sarah , Oca Marcela Montes De , Reis Luiza Campos , Moulik Srija , Walrad Pegine , Chatterjee Mitali , Goto Hiro , Wickremasinghe Renu , Lagos Dimitris , Kaye Paul M. , Ranasinghe Shalindra 
Published: February 2020

AbstractCutaneous leishmaniasis (CL) is a chronic skin disease caused byLeishmaniaparasites and in Sri Lanka, CL is caused byL. donovani.Pentavalent antimonials (e.g. sodium stibogluconate; SSG) are first line drugs for CL, despite protracted and painful treatment regimens. Data from animal models indicate that the effectiveness of SSG requires drug-immune synergy, but mechanistic insight from patients is lacking. We studied whole blood and lesion transcriptomes from CL patients in Sri Lanka at presentation and during SSG treatment. In lesions, we identified differential expression of immune-related genes, including immune checkpoint molecules, after the onset of treatment whereas no differentially expressed genes were identified in whole blood. We confirmed reduced lesional PD-L1 and IDO1 protein expression on treatment in a second validation cohort, using digital spatial profiling and quantitative immunohistochemistry. Dual IHC-FISH revealed significantly higher expression of these immune checkpoint molecules on parasite-infected compared to non-infected lesional CD68+monocytes / macrophages. Crucially, early reduction in PD-L1 but not IDO1 expression was predictive of rate of clinical cure and occurred in parallel with a reduction in parasite load. A multivariate cox proportional hazard model showed that patients with lower PD-L1 expression on treatment were more likely to cure earlier (HR= 4.88). Our data support a model whereby the initial anti-leishmanial activity of antimonial drugs alleviates checkpoint inhibition of T cell immunity, facilitating immune-drug synergism and clinical cure. Our findings demonstrate that PD-L1 expression can be used as an early predictor of clinical response to SSG treatment and support the use of PD-L1 inhibition as adjunct host directed therapy in Sri Lankan CL.
New insights intoTrypanosoma cruzievolution and genotyping based on system-wide protein expression profiles (PhyloQuant)
Authors: Mule Simon Ngao , da Costa Martins Andrè Guillherme , Rosa-Fernandes Livia , de Oliveira Gilberto Santos , Rodrigues Carla Monadeli , Quina Daniel , Rosein Graziella E. , Teixeira Marta Maria Geraldes , Palmisano Giuseppe 
Published: February 2020

AbstractThe etiological agent of Chagas disease,Trypanosoma cruzi, is subdivided into seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance ofT. cruzigenetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution justifies the concerted efforts towards understanding the population structure ofT. cruzistrains. In this study, we introduce a novel approach termed ‘phyloquant’ to infer the evolutionary relationships and assignment ofT. cruzistrains to their DTUs based on differential protein expression profiles evidenced by bottom up large scale mass spectrometry-based quantitative proteomic features. Mass spectrometry features analyzed using parsimony (MS1, iBAQ and LFQ) showed a close correlation between protein expression andT. cruziDTUs and closely related trypanosome species. Although alternative topologies with minor differences between the three MS features analyzed were demonstrated, we show congruence to well accepted evolutionary relationships ofT. cruziDTUs; in all analyses TcI and Tcbat were sister groups, and the parental nature of genotype TcII and the hybrid genotypes TcV/TcVI were corroborated. Character mapping of genetic distance matrices based on phylogenetics and phyloquant clustering showed statistically significant correlations. We propose the first quantitative shotgun proteomics approach as a complement strategy to the genetic-based assignment ofT. cruzistrains to DTUs and evolutionary inferences. Moreover, this approach allows for the identification of differentially regulated and strain/DTU/species-specific proteins, with potential application in the identification of strain/DTU specific biomarkers and candidate therapeutic targets. In addition, the correlation between multi-gene protein expression and divergence of trypanosome species was evaluated, adding another level to understand the genetic subdivisions amongT. cruziDTUs.
A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming
Authors: Ning Daliang , Yuan Mengting , Wu Linwei , Zhang Ya , Guo Xue , Zhou Xishu , Yang Yunfeng , Arkin Adam P. , Firestone Mary K. , Zhou Jizhong 
Published: February 2020

AbstractUnraveling the drivers controlling community assembly is a central issue in ecology. Selection, dispersal, diversification and drift are conceptually accepted as major community assembly processes. Defining their relative importance in governing biodiversity is compellingly needed, but very challenging. Here, we present a novel framework to quantitativelyinfercommunityassemblymechanisms byphylogenetic bin-based null model analysis (iCAMP). Our results with simulated microbial communities showed that iCAMP had high accuracy (0.93 - 0.99), precision (0.80 - 0.94), sensitivity (0.82 - 0.94), and specificity (0.95 - 0.98), which were 10-160% higher than those from the entire community-based approach. Applying it to grassland microbial communities in response to experimental warming, our analysis showed that homogeneous selection (38%) and “drift” (59%) played dominant roles in controlling grassland soil microbial community assembly. Interestingly, warming enhanced homogeneous selection, but decreased “drift” over time. Warming-enhanced selection was primarily imposed on Bacillales in Firmicutes, which were strengthened by increased drought and reduced plant productivity. This general framework should also be useful for plant and animal ecology.
Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus that are Necessary for Synapse Function
Authors: Gokhale Avanti , Lee Chelsea E. , Zlatic Stephanie A. , Freeman Amanda A. H. , Shearing Nicole , Hartwig Cortnie , Ogunbona Oluwaseun , Bassell Julia L. , Wynne Meghan E. , Werner Erica , Xu Chongchong , Wen Zhexing , Seyfried Nicholas , Bearden Carrie E. , Glausier Jill , Lewis David A. , Faundez Victor 
Published: February 2020

AbstractEukaryotic cells maintain proteostasis through mechanisms that require cytoplasmic and mitochondrial translation. Genetic defects affecting cytoplasmic translation perturb synapse development, neurotransmission, and are causative of neurodevelopmental disorders such as Fragile X syndrome. In contrast, there is little indication that mitochondrial proteostasis, either in the form of mitochondrial protein translation and/or degradation, is required for synapse development and function. Here we focus on two genes deleted in a recurrent copy number variation causing neurodevelopmental disorders, the 22q11.2 microdeletion syndrome. We demonstrate that SLC25A1 and MRPL40, two genes present in this microdeleted segment and whose products localize to mitochondria, interact and are necessary for mitochondrial protein translation and proteostasis. OurDrosophilastudies show that mitochondrial ribosome function is necessary for synapse neurodevelopment, function, and behavior. We propose that mitochondrial proteostasis perturbations, either by genetic or environmental factors, are a novel pathogenic mechanism for neurodevelopmental disorders.
Intrinsic growth rules of patients infected, dead and recovered with 2019 novel coronavirus in mainland China
Authors: Han Chuanliang , Liu Yimeng , Yang Saini 
Published: February 2020

AbstractAn outbreak of a novel coronavirus (SARS-CoV-2)-infected pneumonia (COVID-19) was first diagnosed in Wuhan, China, in December 2019 and then spread rapidly to other regions. We collected the time series data of the cumulative number of confirmed infected, dead, and cured cases from the health commissions in 31 provinces in mainland China. A descriptive model in a logistic form was formulated to infer the intrinsic epidemic rules of COVID-19, which illustrates robustness spatially and temporally. Our model is robust (R2>0.95) to depict the intrinsic growth rule for the cumulative number of confirmed infected, dead, and cured cases in 31 provinces in mainland China. Furthermore, we compared the intrinsic epidemic rules of COVID-19 in Hubei with that of severe acute respiratory syndrome (SARS) in Beijing, which was obtained from the Ministry of Public Health of China in 2003. We found that the infected case is the earliest to be saturated and has the lowest semi-saturation period compared with deaths and cured cases for both COVID-19 and SARS. All the three types of SARS cases are later to saturate and have longer semi-saturation period than that of COVID-19. Despite the virus caused SARS (SARS-CoV) and the virus caused COVID-19 (SARS-CoV-2) are homologous, the duration of the outbreak would be shorter for COVID-19.
Community-wide seed dispersal distances peak at low levels of specialisation in size-structured networks
Authors: Sorensen Marjorie C. , Schleuning Matthias , Donoso Isabel , Neuschulz Eike Lena , Mueller Thomas 
Published: February 2020

AbstractNetwork approaches provide insight into the complex web of interspecific interactions that structure ecological communities. However, because data on the functional outcomes of ecological networks are very rarely available, the effect of network structure on ecosystem functions, such as seed dispersal, is largely unknown. Here, we develop a new approach that is able to link interaction networks to a trait-based seed-dispersal model to estimate community-wide seed dispersal distances. We simulated networks, using a niche model based on size-matching between plants and birds, that varied in the degree of niche partitioning. We found that community-wide dispersal distances were longest when networks had low degrees of niche partitioning. We further found that dispersal distances of plant species with small fruits peaked in models without niche partitioning, whereas dispersal distances of medium and large-fruited plants peaked at low degrees of niche partitioning. Our simulations demonstrate that the degree of niche partitioning between species is an important determinant of the ecological functions derived from ecological networks and that simulation approaches can provide new insights into the relationship between the structural and functional components of ecological networks.
Testing the adaptive value of sporulation in budding yeast using experimental evolution
Authors: Thomasson Kelly M. , Franks Alexander , Teotónio Henrique , Proulx Stephen R. 
Published: February 2020

AbstractSaccharomycesyeast can grow through mitotic vegetative cell division while they convert resources in their environment into biomass. When cells encounter specific low nutrient environments, sporulation may be initiated and meiotic division produces 4 haploid cells contained inside a protective ascus. The protected spore state does not acquire new resources but is partially protected from desiccation, heat, and caustic chemicals. Because cells cannot both be protected and acquire resources simultaneously, committing to sporulation represents a trade-off between current and future reproduction. Recent work has suggested that one of the major environmental factors that select for the formation of spores is passaging through insect guts, as this also represents a major way that yeasts are vectored to new food sources. We subjected replicate populations of a panel of 5 yeast strains to repeated, predictable passaging through insects by feeding them to fruit flies (Drosopila melanogaster) and then allowing surviving yeast cell growth in defined media for a fixed period of time. We also evolved control populations using the same predictable growth environments but without being exposed to flies. We assayed populations for their sporulation rate, as measured by the percentage of cells that had sporulated after resource depletion. We found that the strains varied in their ancestral sporulation rate such that domesticated strains had lower sporulation. During evolution, all strains evolved increased sporulation in response to passaging through flies, but domesticated strains evolved to lower final levels of sporulation. We also found that exposure to flies led to an evolved change in the timing of the sporulation response relative to controls, with a more rapid shift to sporulation, and that wild-derived strains showed a more extreme response. We conclude that strains that have lost the ability to access genetic variation for total sporulation rate and the ability to respond to cues in the environment that favor sporulation due to genetic canalization during domestication.
Convergent losses of TLR5 suggest altered extracellular flagellin detection in four mammalian lineages
Authors: Sharma Virag , Walther Felix , Hecker Nikolai , Stuckas Heiko , Hiller Michael 
Published: February 2020

AbstractToll-like receptors (TLRs) play an important role for the innate immune system by detecting pathogen-associated molecular patterns. TLR5 encodes the major extracellular receptor for bacterial flagellin and frequently evolves under positive selection, consistent with coevolutionary arms races between the host and pathogens. Furthermore, TLR5 is inactivated in several vertebrates and a TLR5 stop codon polymorphism is widespread in human populations. Here, we analyzed the genomes of 120 mammals and discovered that TLR5 is convergently lost in four independent lineages, comprising guinea pigs, Yangtze river dolphin, pinnipeds, and pangolins. Validated inactivating mutations, absence of protein-coding transcript expression, and relaxed selection on the TLR5 remnants confirm these losses. PCR analysis further confirmed the loss of TLR5 in the pinniped stem lineage. Finally, we show that TLR11, encoding a second extracellular flagellin receptor, is also absent in these four lineages. Independent losses of TLR5 and TLR11 suggests that a major pathway for detecting flagellated bacteria is not essential for different mammals and predicts an impaired capacity to sense extracellular flagellin
Estimation of risk factors for COVID-19 mortality - preliminary results
Authors: Caramelo F , Ferreira N , Oliveiros B 
Published: February 2020

AbstractSince late December 2019 a new epidemic outbreak has emerged from Whuhan, China. Rapidly the new coronavirus has spread worldwide. China CDC has reported results of a descriptive exploratory analysis of all cases diagnosed until the 11th February 2020, presenting the epidemiologic curves and geo-temporal spread of COVID-19 along with case fatality rate according to some baseline characteristics, such as age, gender and several well-established high prevalence comorbidities. Despite this, we intend to increase even further the predictive value of that manuscript by presenting the odds ratio for mortality due to COVID-19 adjusted for the presence of those comorbidities and baseline characteristics such as age and gender. Besides, we present a way to determine the risk of each particular patient, given his characteristics.We found that age is the variable that presents higher risk of COVID-19 mortality, where 60 or older patients have an OR = 18.8161 (CI95%[7.1997; 41.5517]). Regarding comorbidities, cardiovascular disease appears to be the riskiest (OR= 12.8328 CI95%[10.2736; 15.8643], along with chronic respiratory disease (OR=7.7925 CI95%[5.5446; 10.4319]). Males are more likely to die from COVID-19 (OR=1.8518 (CI95%[1.5996; 2.1270]). Some limitations such as the lack of information about the correct prevalence of gender per age or about comorbidities per age and gender or the assumption of independence between risk factors are expected to have a small impact on results. A final point of paramount importance is that the equation presented here can be used to determine the probability of dying from COVID-19 for a particular patient, given its age interval, gender and comorbidities associated.
Non-existent ClinicalTrials.gov identifiers in abstracts indexed by PubMed
Authors: Carlisle Benjamin Gregory 
Published: February 2020

AbstractProspective registration plays an important role in ensuring the transparency and reliability of clinical trials. Preregistration of clinical trials has been required by the ICMJE since 2005 and mandated by law for most clinical trial types since 2007. It is one of the roles of peer reviewers of a clinical trial publication to confirm that there is concordance between the registry entry and the submitted publication. On October 22, 2019, abstracts for all articles indexed by PubMed with publication type “Clinical Trial” and a publication date after January 1, 2003 were downloaded. Clinical trial registry identifiers were automatically extracted and tested for the existence of a corresponding entry on ClinicalTrials.gov. Among 38,001 published clinical trial registry numbers, 215 (0.6%) do not correspond to a legitimate clinical trial registry entry. While there is a small proportion of non-existent NCT numbers in our sample, even a single non-existent NCT number in a publication represents a failure on the part of journals who publish clinical trials to systematically ensure that reviewers always check clinical trial registry entries for concordance with the text submitted for publication. These results cast doubt on how frequently editors and reviewers evaluate clinical trial reports in light of their corresponding registry entries.
Multidimensional Analysis of Bronchoalveolar Lavage Cytokines and Mast Cell Proteases Reveals Interferon-γ as a Key Biomarker in Equine Asthma Syndrome
Authors: Woodrow Jane S. , Hines Melissa , Sommardahl Carla , Flatland Bente , Davis Kaori U. , Lo Yancy , Wang Zhiping , Sheats Mary Katherine , Lennon Elizabeth M. 
Published: February 2020

AbstractNaturally-occurring equine asthma is an inflammatory lung disease characterized by chronic, partially reversible airway obstruction, pulmonary remodeling and lower airway inflammation. The cytokine profiles that distinguish asthma groups or subtypes in horses have not been systematically classified, and mast cell phenotypes, which, in human asthma, correlate with asthma type, lung function, and response to therapy, have not been well-described in horses. The purpose of this study was to: (1) compare mast cell protease mRNA expression between healthy and asthmatic horses, (2) analyze the cytokine profile present in BALF of currently defined equine asthma groups, and (3) use these data to evaluate potential biomarkers of defined asthma groups. Mast cell protease gene expression and select cytokine gene expression in cells isolated from BALF, and BALF multiplex cytokine assays were performed. Multidimensional analysis demonstrated that IFNγ differentiates severe from moderate asthma, and that TNFα and CXCL8 are key biomarkers of equine asthma subtype. Expression of chymase mRNA, a mast cell-specific protease, was significantly decreased in horses with mastocytic asthma. These results will help further define EAS immunopathology, which could improve understanding and definitions of asthma groups, while also potentially identify novel therapeutic strategies.